[med-svn] [psortb] branch master updated (b0700ac -> 7d4999b)

[Andreas Tille]

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tille pushed a change to branch master
in repository psortb.

      from  b0700ac   Use libsquid
       new  0101c59   Remove copies of hmmer2 header files and use libhmmer2-dev instead
       new  65617d0   New upstream version 3.0.4+dfsg
       new  92e9029   Merge tag 'upstream/3.0.4+dfsg'
       new  6939821   Remove now useless patch since libhmmer2-dev contains patched header
       new  13eb506   Use `pkg-config --cflags libhmmer2` from libhmmer2-dev package
       new  accaccd   Adapt to hmmer2 interface
       new  b91dba4   Adapt to hmmer2 interface
       new  7d4999b   Fix C++ syntax issue (thanks to Walter Landry)

The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 algorithm-hmm/src/include/config.h               |  52 ---
 algorithm-hmm/src/include/funcs.h                | 350 --------------
 algorithm-hmm/src/include/globals.h              |  28 --
 algorithm-hmm/src/include/gsi.h                  |  85 ----
 algorithm-hmm/src/include/gsi64.h                | 101 ----
 algorithm-hmm/src/include/postprob.h             |  55 ---
 algorithm-hmm/src/include/structs.h              | 565 -----------------------
 debian/control                                   |   3 +-
 debian/copyright                                 |   6 +
 debian/patches/biosquid_includes.patch           |   2 +-
 debian/patches/fix_hmmer_interface.patch         |  51 ++
 debian/patches/series                            |   2 +-
 debian/patches/use_declaration_of_biosquid.patch |  14 -
 13 files changed, 61 insertions(+), 1253 deletions(-)
 delete mode 100644 algorithm-hmm/src/include/config.h
 delete mode 100644 algorithm-hmm/src/include/funcs.h
 delete mode 100644 algorithm-hmm/src/include/globals.h
 delete mode 100644 algorithm-hmm/src/include/gsi.h
 delete mode 100644 algorithm-hmm/src/include/gsi64.h
 delete mode 100644 algorithm-hmm/src/include/postprob.h
 delete mode 100644 algorithm-hmm/src/include/structs.h
 create mode 100644 debian/patches/fix_hmmer_interface.patch
 delete mode 100644 debian/patches/use_declaration_of_biosquid.patch

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